Persistent extreme precipitation events (PEPEs) in Southeast China cause casualties and economic losses, and accurate simulations of these events continue to face significant challenges. This study identifies critical features associated with PEPEs during boreal summer in this region, such as both cool land surface and air at 850 hPa, indicating strong land‐atmosphere interactions. Vertical soil water flow (VSWF) significantly affects near‐surface soil hydro‐thermodynamics and can potentially enhance the PEPEs' simulation. However, VSWF is often ignored in land surface models. To improve the simulation of PEPEs, the VSWF term is incorporated into the soil heat transfer equation within the Noah‐MP model coupled with the Weather Research and Forecasting model, improving the simulation of PEPEs. Further analysis reveals that incorporating VSWF strengthens the cold features of PEPEs and improves precipitation simulation. Detailed examination shows that incorporating VSWF induces a secondary circulation anomaly and a positive geopotential height anomaly in Southeast China compared to simulations without VSWF. The southeast flank of the anticyclone anomaly reduces water vapor transport, while the northwest flank enhances it. Additionally, the geopotential height anomaly triggers adjustments in downstream regions of Southeast China, depending on changes in downstream circulation patterns of PEPEs. This research contributes to a better understanding of land‐atmosphere interactions, particularly the effects of VSWF on PEPEs in Southeast China.